title: Terahertz absorption of DNA decamer duplex.
abstract: This work combines experimental and theoretical approaches to investigate terahertz absorption spectra of the DNA formed by the sequence oligomer 5'-CCGGCGCCGG-3'. The three-dimensional structure of this self-complimentary DNA decamer has been well-studied, permitting us to perform direct identification of the low-frequency phonon modes associated with specific conformation and to conduct comprehensive computer simulations. Two modeling techniques, normal-mode analysis and nanosecond molecular dynamics with explicit solvent molecules, were employed to extract the low-frequency vibrational modes based on which the absorption spectra were calculated. The absorption spectra of the DNA decamer in aqueous solution were measured in the frequency range 10-25 cm(-1) using the terahertz Fourier transform infrared spectroscopy. Multiple well-resolved and reproducible resonance modes were observed. When calculated and experimental spectra were compared, the spectrum based on molecular dynamics simulations showed a better correlation with the experimental spectra than the one based on normal-mode analysis. These results demonstrate that there exist a considerable number of active low-frequency phonon modes in this short DNA duplex.
authors.affiliation: Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, Virginia 22904, USA.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Li
authors.forename: Tatiana
authors.initials: T
authors.lastname: Globus
authors.forename: Boris
authors.initials: B
authors.lastname: Gelmont
authors.forename: Luiz C
authors.initials: LC
authors.lastname: Salay
authors.forename: Alexei
authors.initials: A
authors.lastname: Bykhovski
mesh_terms: D000042:Absorption; D001483:Base Sequence; D002942:Circular Dichroism; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000235:genetics
chemical_list: D009838:Oligodeoxyribonucleotides; D004247:DNA